Clean up Click testing

tests/experiment/tools/test_nidm_lingreg.py

@@ -1,63 +1,26 @@
 from __future__ import annotations
 from pathlib import Path
-import click
 from click.testing import CliRunner
 import pytest
 from nidm.experiment.tools.nidm_linreg import linear_regression
 
 
-def call_click_command(cmd, *args, **kwargs):
-    """Wrapper to call a click command
-
-    :param cmd: click cli command function to call
-    :param args: arguments to pass to the function
-    :param kwargs: keyword arguments to pass to the function
-    :return: None
-    """
-
-    # Get positional arguments from args
-    arg_values = {c.name: a for a, c in zip(args, cmd.params)}
-    args_needed = {c.name: c for c in cmd.params if c.name not in arg_values}
-
-    # build and check opts list from kwargs
-    opts = {a.name: a for a in cmd.params if isinstance(a, click.Option)}
-    for name in kwargs:
-        if name in opts:
-            arg_values[name] = kwargs[name]
-        else:
-            if name in args_needed:
-                arg_values[name] = kwargs[name]
-                del args_needed[name]
-            else:
-                raise click.BadParameter("Unknown keyword argument '{}'".format(name))
-
-    # check positional arguments list
-    for arg in (a for a in cmd.params if isinstance(a, click.Argument)):
-        if arg.name not in arg_values:
-            raise click.BadParameter(
-                "Missing required positional parameter '{}'".format(arg.name)
-            )
-
-    # build parameter lists
-    opts_list = sum([[o.opts[0], arg_values[n]] for n, o in opts.items()], [])
-    args_list = [str(v) for n, v in arg_values.items() if n not in opts]
-
-    # call the command
-    CliRunner().invoke(cmd, opts_list + args_list)
-
-
-def test_simple_model(brain_vol_files: list[str], tmp_path: Path) -> None:
-    arguments = dict(
-        nidm_file_list=",".join(brain_vol_files),
-        ml="fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
-        ctr=None,
-        regularization=None,
-        output_file=str(tmp_path / "output.txt"),
-    )
-
-    call_click_command(linear_regression, *arguments, **arguments)
-
-    out = (tmp_path / "output.txt").read_text()
+def test_simple_model(brain_vol_files: list[str]) -> None:
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        r = runner.invoke(
+            linear_regression,
+            [
+                "--nidm_file_list",
+                ",".join(brain_vol_files),
+                "--ml",
+                "fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
+                "-o",
+                "output.txt",
+            ],
+        )
+        assert r.exit_code == 0
+        out = Path("output.txt").read_text()
 
     # check if model was read correctly
     assert "fs_000008 ~ ilx_0100400 + DX_GROUP" in out
@@ -80,20 +43,26 @@ def test_simple_model(brain_vol_files: list[str], tmp_path: Path) -> None:
     )
 
 
-def test_model_with_contrasts(brain_vol_files: list[str], tmp_path: Path) -> None:
+def test_model_with_contrasts(brain_vol_files: list[str]) -> None:
     # run linear regression tool with simple model and evaluate output
 
-    arguments = dict(
-        nidm_file_list=",".join(brain_vol_files),
-        ml="fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
-        ctr="DX_GROUP",
-        regularization=None,
-        output_file=str(tmp_path / "output.txt"),
-    )
-
-    call_click_command(linear_regression, *arguments, **arguments)
-
-    out = (tmp_path / "output.txt").read_text()
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        r = runner.invoke(
+            linear_regression,
+            [
+                "--nidm_file_list",
+                ",".join(brain_vol_files),
+                "--ml",
+                "fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
+                "--ctr",
+                "DX_GROUP",
+                "-o",
+                "output.txt",
+            ],
+        )
+        assert r.exit_code == 0
+        out = Path("output.txt").read_text()
 
     # check if model was read correctly
     assert "fs_000008 ~ ilx_0100400 + DX_GROUP" in out
@@ -147,20 +116,26 @@ def test_model_with_contrasts(brain_vol_files: list[str], tmp_path: Path) -> Non
 @pytest.mark.skip(
     reason="regularization weights seem to be different depending on the platform"
 )
-def test_model_with_contrasts_reg_L1(
-    brain_vol_files: list[str], tmp_path: Path
-) -> None:
-    arguments = dict(
-        nidm_file_list=",".join(brain_vol_files),
-        ml="fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
-        ctr="DX_GROUP",
-        regularization="L1",
-        output_file=str(tmp_path / "output.txt"),
-    )
-
-    call_click_command(linear_regression, *arguments, **arguments)
-
-    out = (tmp_path / "output.txt").read_text()
+def test_model_with_contrasts_reg_L1(brain_vol_files: list[str]) -> None:
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        r = runner.invoke(
+            linear_regression,
+            [
+                "--nidm_file_list",
+                ",".join(brain_vol_files),
+                "--ml",
+                "fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
+                "--ctr",
+                "DX_GROUP",
+                "--regularization",
+                "L1",
+                "-o",
+                "output.txt",
+            ],
+        )
+        assert r.exit_code == 0
+        out = Path("output.txt").read_text()
 
     # check if model was read correctly
     assert "fs_000008 ~ ilx_0100400 + DX_GROUP" in out
@@ -179,20 +154,26 @@ def test_model_with_contrasts_reg_L1(
 @pytest.mark.skip(
     reason="regularization weights seem to be different depending on the platform"
 )
-def test_model_with_contrasts_reg_L2(
-    brain_vol_files: list[str], tmp_path: Path
-) -> None:
-    arguments = dict(
-        nidm_file_list=",".join(brain_vol_files),
-        ml="fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
-        ctr="DX_GROUP",
-        regularization="L2",
-        output_file=str(tmp_path / "output.txt"),
-    )
-
-    call_click_command(linear_regression, *arguments, **arguments)
-
-    out = (tmp_path / "output.txt").read_text()
+def test_model_with_contrasts_reg_L2(brain_vol_files: list[str]) -> None:
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        r = runner.invoke(
+            linear_regression,
+            [
+                "--nidm_file_list",
+                ",".join(brain_vol_files),
+                "--ml",
+                "fs_000008 = DX_GROUP + http://uri.interlex.org/ilx_0100400",
+                "--ctr",
+                "DX_GROUP",
+                "--regularization",
+                "L2",
+                "-o",
+                "output.txt",
+            ],
+        )
+        assert r.exit_code == 0
+        out = Path("output.txt").read_text()
 
     # check if model was read correctly
     assert "fs_000008 ~ ilx_0100400 + DX_GROUP" in out